[BioC] failing to filter ExpressionSet object using nsFilter
Martin Morgan
mtmorgan at fhcrc.org
Sat Jul 5 21:38:16 CEST 2014
Hi David --
On 07/05/2014 05:49 AM, David [guest] wrote:
> Dear all,
>
> I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse Gene 2.1), based on low filtering. This object was generated using the "rma" function. However, I get this:
>
>> filtered <- nsFilter(myExpressionSet, var.filter=FALSE)
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function ‘columns’ for signature ‘"AffyGenePDInfo"’
This is likely a version mismatch between the annotation package per se (pd.*)
and the AnnotationDbi package.
BiocInstaller::biocValid()
might suggest packages that are either too old or too new for your installation.
Updating to R-3.1 is also an option, which would imply updating all packages to
the current Bioconductor release.
Martin
>
>
> Any ideas how to troubleshoot this?
>
> Thanks,
> David
>
> -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 mogene21stprobeset.db_2.13.0
> [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 pathview_1.2.4
> [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 KEGGgraph_1.20.0
> [10] graph_1.40.1 XML_3.95-0.2 KEGGREST_1.2.2
> [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7
> [16] limma_3.18.13 oligo_1.26.6 Biostrings_2.30.1
> [19] XVector_0.2.0 IRanges_1.20.7 oligoClasses_1.24.0
> [22] genefilter_1.44.0 affy_1.40.0 Biobase_2.22.0
> [25] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 bit_1.1-12
> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.14.4
> [9] httr_0.3 iterators_1.0.7 png_0.1-7 preprocessCore_1.24.0
> [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 stats4_3.0.2
> [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 xtable_1.7-3
> [21] zlibbioc_1.8.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
More information about the Bioconductor
mailing list